title: BCC_W_2,scRNAseq

city: Epalinges

first: Laura

last: Yerly

address: Chemin de Boveresses 155

country: Switzerland

institute: CHUV

description: 10X Genomics

data_processing:
Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (v. 2.20, Illumina). Raw sequencing data provided as fastq files were processed using the count function of the Cell Ranger pipeline (v. 7.1.0, 10x Genomics). The count function allowed us to demultiplex reads to individual cells, to align the reads to the human GRCh38 reference (v. GRCh38-2020-A), and to generate filtered matrices of gene counts by cell barcodes.
Assembly: hg18
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skin

extract_protocol:
Fresh tumor tissue was minced and enzymatically digested to obtain a single cell suspension. Single living cells were then FACS sorted. The cells were resuspended to reach a target final concentration of approximately 1,000 cells/μl. ScRNA-seq was performed using the Chromium Next GEM single cell 3' reagent kit v3.1 (10xGenomics) following the manufacturer's protocol with a target number of captured cells of 10,000.
Sequencing libraries were prepared after GEM generation and barcoding using the Chromium Next GEM single cell 3'reagent kit v3.1 (10xGenomics) the following manufacturer's protocol.

value: Skin

tag: subject id

value: Patient 2

tag: tumor subtype

value: nodular basal cell carcinoma

tag: condition

value: Wounded


title: BCC_UW_2,scRNAseq

status: Public on May 31 2024

type: SRA

description: 10X Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: Unwounded


title: 25-4-H3K27me3-R2

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

country: USA

institute: Virginia Tech

library_source: genomic

data_processing:
Raw ChIP-seq reads were aligned to hg19 genome by bwa (0.7.17).
Aligned reads were deduplicated and those with MAPQ>=10 were retained.
Narrow peaks (H3K27ac, H3K4me1, H3K4me3) were called by MACS2 (2.2.7.1) with q-value<=0.05. Board peaks (H3K27me3, H3K9me3) were called by Homer findPeaks in histone mode with p-value<=0.05.
Raw RNA-seq reads were trimmed by Trim Galore.
Trimmed RNA-seq reads were aligned to hg19 genome by STAR.
Assembly: hg19
Supplementary files format and content: bigwig track files (ChIP-seq)
Supplementary files format and content: txt gene read count files (RNA-seq)

molecule: genomic DNA

source_name: Lung

extract_protocol:
Nuclei extraction: Samples were shipped to Virginia Tech on dry ice and stored in liquid nitrogen vapor phase until use. Thin slices were cut from the tissue on dry ice with a sharp scalpel and transferred to the grinder (D9063, Sigma-Aldrich) pre-cooled on ice. Subsequent steps were performed on ice and centrifugation performed at 4°C. 3 ml of ice-cold nuclei extraction buffer [0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM tris-HCl, and 0.1% Triton X-100, with 30 µl of PIC (P8340, Sigma-Aldrich), 3 µl of 100 mM PMSF, and 3 µl of 1 M dithiothreitol added before use] was added to the grinder. Tissue was homogenized by slowly douncing 20 times with pestle A and 30 times with pestle B. Homogenate was filtered through a 40 µm cell strainer into a 15 ml tube and centrifuged at 1000g for 10 min. Supernatant was removed and the crude nuclei pellet was resuspended in 500 µl nuclei extraction buffer and transferred to a 1.5 ml tube. 750 µl of 50% iodixanol, 7.5 µl of PIC, 0.75 µl of 100 mM PMSF and 0.75 µl of 1M dithiothreitol were added and mixed by gently pipetting and then inverting the tube five times. The mixture was centrifuged at 10,000g for 20 min and the supernatant was removed. The purified nuclei pellet was resuspended in 200 µl of Dulbecco's phosphate-buffered saline (DPBS).  MNase digestion of chromatin: Resuspended nuclei were counted and diluted to 4×10^6/ml if needed. 2 µl of PIC, 2 µl of 100 mM PMSF and 200 µl lysis buffer [4% Triton X-100, 100 mM tris-HCl, 100 mM NaCl, and 30 mM MgCl2] were added to 200 µl of nuclei suspension, mixed by vortexing and incubated at room temperature for 10 min. 20 µl of 100 mM CaCl2 and 5 µl of 100U MNase (88216, Thermo Fisher Scientific) were added, mixed by vortexing and incubated at room temperature for 10 min. 44 µl of 0.5 M EDTA was then added, mixed by vortexing and incubated on ice for 10 min. The solution was centrifuged at 16,100g for 5 min at 4°C. Supernatant containing chromatin fragments were transferred to a new 1.5 ml tube and placed on ice. 30 µl of chromatin solution was used for each ChIP assay (~50K nuclei).  Preparation of immunoprecipitation beads: 5 µl of protein A Dynabeads (10001D, Invitrogen) were used in each MOWChIP assay. The beads were washed twice with IP buffer (20 mM tris-HCl, pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% (w/v) sodium deoxycholate, 0.1% SDS, 1% (v/v) Triton X-100) and resuspended in 150 µl of IP buffer. The following antibodies were used in this work: anti-H3K27ac (ab4729, Abcam), 0.125 µg/assay; anti-H3K4me1 (39297, Active Motif), 0.5 µl/assay; anti-H3K4me3 (ab8580, Abcam), 0.125 µg/assay; anti-H3K27me3 (39155, Active Motif), 0.5 µg/assay; anti-H3K9me3 (ab8898, Abcam), 0.125 µg/assay. The suspension was incubated on a rotator at 4°C overnight. The beads were washed with IP buffer twice and resuspended in 5 µl of IP buffer for loading in the MOWChIP device.  MOWChIP: The microfluidics based MOWChIP process, including device fabrication and operation, was performed following our published protocol (Zhu, B., Hsieh, YP., Murphy, T.W. et al. MOWChIP-seq for low-input and multiplexed profiling of genome-wide histone modifications. Nat Protoc 14, 3366–3394 (2019).).  RNA extraction: Tissue slices were placed in 200 µl of RNAlater-ICE frozen tissue transition solution (AM7030, Thermo Fisher Scientific) prechilled to -80°C. They were then incubated at -20°C overnight. Each RNA-seq library was prepared from 10ng RNA extracted from the tissue. Two technical replicates were prepared for each sample. Total RNA was extracted from the incubated tissue using the RNeasy Mini Kit (74104, Qiagen) and RNase-Free DNase Set (79254, Qiagen).
ChIP-seq: Libraries were prepared using 2S Plus DNA library kit (IDT) following the manufacturer’s protocol. 1 × EvaGreen dye (Biotium) was added to the qPCR amplification mixture to monitor progress of amplification. Library was eluted to 7 µl of low EDTA TE buffer. Library size distribution was examined using TapeStation (Agilent) and concentration was quantified with Kapa Library Quantification kit (Kapa Biosystems).  RNA-seq: Extracted total RNA was resuspended in 4.5 μL of RNase-free water with 5% RNase inhibitor (40 U/μL) added. 2 μL of oligo-dT primer (10 μM), 2 μL of dNTP mix (10 mM) and 4.3 μL of total RNA solution were mixed, incubated at 72°C for 3 minutes and immediately put on ice. Then 1 μL of SuperScript II reverse transcriptase (200 U/μL), 0.5μL of RNase inhibitor (40 U/μl), 4μL of Superscript II first-strand buffer, 1 μL of DTT (100 mM), 4 μL of 5 M Betaine, 0.12 μL of 1 M MgCl2, 0.2 μL of TSO (100 μM), 0.88 μL of nuclease-free water were added to the 8.3 μl mixture mentioned above. The reverse transcription (RT) reaction mix was then incubated at 42°C for 90 minutes, followed by 10 cycles of 50°C for 2 minutes and 42°C for 2 minutes, and lastly 70°C for 15 minutes. The RT reaction mix was mixed with 25 μL KAPA HiFi HotStart ReadyMix, 0.5 μL IS PCR primers (10 μM), 2.5 μL Evagreen dye, and 2 μL nuclease-free water, and amplified with: 98°C for 1 minute, 9–11 cycles of 98°C 15 seconds, 67°C 30 seconds, 72°C 6 minutes. The cDNA was purified using 30 μL of SPRIselect beads and eluted in 5 μL of low EDTA TE buffer. The RNA-seq library was made using tagmentation. 3 μL of home-made Tn5 was mixed with 3 μL of 50 μM pre-annealed P5/P7 transposon and incubated at 37°C for 1 hour. Assembled P5 and P7 transposons were then mixed well to form Tn5 mix. 1 μL cDNA (600 pg) and 1 μL of tagmentation buffer (TNP92110, Lucigen) were added to 8 μL Tn5 mix, and the mixture was incubated at 37°C for 1 hour. 1 μL of 10X stop buffer (TNP92110, Lucigen) was then added to the mixture to quench tagmentation. 11 μL SPRIselect beads were used to purify tagmented cDNA. The cDNA was then eluted in 9.5 μL of low EDTA TE buffer. 25 μL of KAPA HiFi HotStart ReadyMix was incubated at 98°C for 30 seconds, mixed with 9.5 μL tagmented cDNA and incubated at 72°C for 5 minutes. 1.5 μL of 100 μM P5 primer, 1.5 μL of 100 μM P7 primer, 10 μL nuclease-free water and 2.5 μL Evagreen were then added and amplified with: 98°C for 30 seconds; 10-12 cycles of 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 30 seconds. Amplified cDNA libraries were purified with 50 μL SPRIselect beads and eluted in 8 μL of low EDTA TE buffer. The RNA library preparation is adapted from Smart-Seq2 workflow (Picelli, S., Faridani, O., Björklund, Å. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 9, 171–181 (2014).)

value: Lung

tag: disease state

value: Tumor

tag: chip antibody

value: H3K27me3 (Active Motif, #39155)


title: APCTom_P2

city: Minato City, Tokyo

first: Teh-Wei

last: Wang

address: 4 Chome-6-1 Shirokanedai

country: Japan

institute: IMSUT

library_source: transcriptomic

data_processing:
After size selection and PCR enrichment, the RNA library was sequenced on Illumina platforms.  The sequencing data were aligned to a mouse reference genome (mm10) using Rsubread (version 2.4.3) 39. Raw counts were obtained from read alignments through refGene, and then further transferred into CPM by edgeR (version 3.32.1) 40. After filtering out low-expression genes with CPM lower than 10, differential expression was analyzed with the linear model using limma (version 3.46.0) 34. Genes with log2FC>1 and FDR<0.05 adjusted by B-H method were considered as significant differentially expressed genes (DEGs)
Assembly: mm10
Supplementary files format and content: align_fc.Rdata

organism: Mus musculus

source_name: Gonadal adipose tissue

extract_protocol:
Gonadal adipose tissue samples were subjected to direct mincing using a sharp scissor, followed by digestion in DMEM supplemented with 0.3 unit/ml Liberase TM (Roche) and 10% BSA at 37°C for 50 min with gentle shaking. After incubation, the resulting cell suspension was centrifuged at 400g for 3 min, and the supernatant was removed. The stromal vascular fractions (SVFs) present in the cell pellet were resuspended in DMEM and passed through 100 µm cell strainers. Subsequently, the red blood cells were lysed using RBC buffer for 5 min. The remaining cells were washed with PBS and resuspended in PBS containing 4% FBS and mouse FcR blocking reagent (MACS) at 4°C for 10 min, and further stained with anti-CD31antibodies and anti-CD45 antibody at 4°C for 30 min, washed and  passed through 70 µm cell strainers and then subjected to FACS SORP Aria (BD Biosciences) to sort out cells.The total RNA of sorted Tom+ and Tom- APCs from tumor bearing mice was extracted by using Single Cell RNA Purification Kit (NORGEN) according to the manufacturer’s instructions.
Total RNA were submitted to Novogene (China) and reverse transcribed into the cDNA library. Then the cDNA samples were fragmented, end-repaired, A-tailed, and ligated with adaptors.

value: Gonadal adipose tissue

tag: cell type

value: Adipocyte progenitor cells

tag: sorted cells

value: tdTomato-positive

tag: genotype


title: 25-4-H3K27me3-R1


title: BCC_UW_1,scRNAseq

description: 10X Genomics

value: Patient 1


title: APCTom_N3

value: tdTomato-negative


title: 25-34-H3K27me3-R1


title: APCTom_N2


title: BCC_W_1,scRNAseq

description: 10X Genomics


title: APCTom_N1


title: 25-5-H3K27me3-R2


title: BCC_B_1,scRNAseq

description: 10X Genomics

value: Baseline


title: 25-33-H3K27me3-R1


title: 25-33-H3K27me3-R2


title: 25-32-H3K27me3-R1


title: 819DNA

city: Piscataway

first: Alison

middle: I

last: Bernstein

state: NJ

address: 170 Freylinghuysen Rd

department: Pharmacology and Toxicology

institute: Rutgers University

data_processing:
Adapter trimming: Read adapters were trimmed using the trim_galore tool (version 0.4.5). In trim_galore, we used the default minimum quality score and added a stringency value of 6, thereby requiring a minimum overlap of 6 bp.
Read alignment: Reads were aligned to the mm10 genome using bismark (version 0.19.1) and bowtie2 (version 2.3.2) with default parameters.
Coverage file generation: Methylation data was extracted from the aligned reads in bismark (version 0.19.1) using a minimum threshold of 5 reads to include a CpG site in analysis.
Assembly: mm10
Supplementary files format and content: Bismark coverage files (.cov.gz) contain % methylation beta values for CpG sites with sequencing coverage.

source_name: Mouse midbrain

extract_protocol:
DNA was isolated from tissue punches using Qiagen QIAamp DNA Micro Kits (Qiagen, Cat. # 56304) according to manufacturer instructions for Isolation of Genomic DNA from Tissues with the following modifications and optional steps included to increase yield. Prior to addition of ATL buffer to punches, 80 µL PBS was added and a 1.5 mL tube pestle was used to manually homogenize the sample. 100 µL ATL buffer was added to each sample. For the proteinase K digestion step, samples were incubated at 56°C overnight. Carrier RNA was added to Buffer AL. The incubation time after addition of 100% EtOH was increased to 10 minutes. The incubation time for the elution step was increased to 5 minutes and this step was repeated a second time. DNA was eluted in 54 µL of 10 mM Tris-HCl, pH 8.0.
SeqCap Epi custom bait probes for regions of interest were designed using the Roche NimbleDesign software.Capture hybridization-sequencing libraries were prepared by the Van Andel Institute Genomics Core from 100 ng of high molecular weight DNA using the Accel-NGS Methyl-Seq DNA Library kit (v3.0) (Swift Biosciences, Cat. #30024). DNA was sheared following manufacturer’s protocol to an average size of 250bp, and sheared DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (Zymo Research, Cat. #D5005) with an elution volume of 15 µL. Following adapter ligation, 8 cycles of library amplification were performed. Amplified libraries were pooled in batches of 8 and targeted enrichment of our custom regions was performed using Roche SeqCap Epi developer probes (Supplementary File 1) and SeqCap HyperEpi workflow starting at step 4.0 with the following modifications. The capture was performed using IDT xGen Universal blockers to replace the SeqCap HE Universal Oligo and SeqCap HE Index Oligo. The post-capture amplification was also adjusted to 11 cycles of amplification and the final extension changed from 30 seconds to 1 minute. Quality and quantity of the finished library pools were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.) and QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA. Sequencing (100 bp, paired end) was performed on an Illumina NovaSeq6000 sequencer using an S4, 200 bp sequencing kit (Illumina Inc., San Diego, CA, USA) with 10% PhiX included to improve base diversity. Base calling was done by Illumina Real Time Analysis 3 and output of NextSeq Control Software was demultiplexed and converted to FastQ format with the Illumina Bcl2fastq software (version 1.9.0).
Capture hybridization sequencing (targeted bisulfite-seq)

value: Mouse midbrain

tag: strain

tag: Sex

value: Male

tag: age

value: 36 weeks

tag: treatment

value: Control


title: 818DNA

value: Dieldrin


title: C-04-0018

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
CellRanger version 6.1.2 was applied to the combined scRNA-Seq, HTO and ADT FASTQ files, alinged to both the hg38 and hg19 genomes. Example: cellranger count --id=$INPUTFILE --libraries=library.csv --transcriptome=/database/cellranger/$SPECIESDATABASE --feature-ref=$ADT-feature.csv --localmem 132 --chemistry SC3Pv3HT (for HT experiment)
SoupX ambient RNA removal was perfomred using an estimated contamination fraction of 15% on all samples.
The CITE-Seq filtered 10x Genomics count matrices from Cell Ranger underwent ambient RNA correction using the software SoupX, with a target contamination fraction of 15% (PMC7763177). Cell barcodes were subsequently filtered using the python scanpy package v 1.9.3 to retain cells expressing >300 genes, read counts >500 and mitochondrial content <20%. The resulting counts were normalized for each cell as counts per ten thousand (CPTT) reads and input to cellHarmony for reference-based classification against 89 stable healthy human bone marrow progenitor reference cell populations (PMC11003869). Projection of cells into this healthy atlas was performed by associating each cellHarmony cell with a random representative cell in the reference atlas UMAP coordinates with a random offset (approximateUMAP function in AltAnalyze). Differential gene expression comparative analyses were performed in cellHarmony using an empirical Bayes moderated t-test (p<0.01) and fold>1.2, considering reduced pseudobulk expression vectors for each patient and annotated cell population, in which at least 10 cells were present. Gene set enrichment analyses were performed using the software GO-Elite in AltAnalyze, using the Ensembl version 100 database, to report minimally non-redundant Gene Ontology associations (PMC3413395).
Assembly: hg38
Supplementary files format and content: CellRanger filtered HDF5 sparse count matrix

source_name: Bone Marrow

extract_protocol:
Cells were isolated from frozen bone marrow. Total nucleated cells were live and dead sorted on Sony MA900. ficoled and enriched for CD34+ cells with double column setup on AutoMACS. The CITE-Seq library included 34 Biolegend TotalSeq-A antibodies.
The CITE-Seq library construction protocol followed the Biolegend 10X 3' V3.1 single index ADT protocol and 10X 3' V3.1 dual index protocol, with additional modifications.
Dual-indexed transcriptome libraries were pooled and sequenced across multiple Illumina Novaseq 6000 S4 or X plus flow cells (Illumina) with PE150+10+10 or PE100+10+10 settings. Single indexed ADT libraries were pooled and sequenced on Illumina S2 flow cells with PE50+8 setting or with transcriptome libraries.

value: Bone Marrow

tag: ancestry

value: African Ancestry

value: male

value: NPM1c Mutated abnormal AML

value: Pretreatment

tag: survival <1_year

value: Yes


title: C-01-0171

value: NPM1c Mutated CN-AML


title: C-05-1893


title: C-94-376

value: female

value: No


title: BCC_B_2,scRNAseq

description: 10X Genomics

value: Skin

value: Patient 2

value: nodular basal cell carcinoma


title: 25-31-H3K27me3-R2

value: Lung

value: Tumor

value: H3K27me3 (Active Motif, #39155)


title: 817DNA

value: Mouse midbrain

value: Male

value: 36 weeks

value: Control


title: 25-31-H3K27me3-R1


title: C-08-0817

value: Bone Marrow

value: European Ancestry

value: male


title: 25-30-H3K27me3-R2


title: APCTom_P1

value: Gonadal adipose tissue

value: Adipocyte progenitor cells

value: tdTomato-positive


title: 815DNA


title: C-08-1102

value: NPM1c Mutated Sole -Y

value: Pretreatment

value: No


title: 25-34-H3K27me3-R2


title: 814DNA

value: Dieldrin


title: 25-30-H3K27me3-R1

value: Lung


title: 813DNA


title: C-07-2140

value: female

value: NPM1c Mutated CN-AML


title: 25-29-H3K27me3-R2

value: Tumor

value: H3K27me3 (Active Motif, #39155)


title: 25-32-H3K27me3-R2


title: 25-29-H3K27me3-R1


title: C-06-0596

value: Yes


title: 812DNA

value: Mouse midbrain

value: Male

value: 36 weeks


title: C-00-1827

value: Bone Marrow

value: African Ancestry


title: 816DNA


title: Geriatric TA Muscle, 5dpi

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: 237 Tower Road

department: Biomedical Engineering

institute: Cornell University

data_processing:
Raw sequencing reads were processed with the slide-snake pipeline (https://github.com/mckellardw/slide_snake).Briefly we trimmed the reads (adapters, low quality reads etc) (cutadapt version 4.6) and mapped to the mouse genome (GRCm39) using the STAR Solo (STAR version 2.7.10b) pipeline that generates a feature-by-bead barcode expression matrix.
Assembly: GRCm39
Supplementary files format and content: HDF5 file containing raw gene expression count matrix (UMI counts) per bead barcode

molecule: polyA RNA

source_name: Tibialis Anterior Muscle

extract_protocol:
Slide-seq Spatial Transcriptomics libraries for young and geriatric TA muscle sections were prepared using the Curio Seeker Spatial Transcriptomics kit (Curio Biosciences), following the manufacturer's instructions. Briefly, fresh-frozen tissue was mounted on 3mm x 3mm Curio Seeker tiles, followed by RNA hybridization, reverse transcription, enzymatic digestion, and bead detachment from the glass tiles. This was followed by second strand cDNA synthesis and amplification.
The cDNA ibraries were prepared with the Nextera XT DNA sample preparation kit following Curio instructions. The samples were then pooled and sequenced on an Illumina NextSeq 2K system with a P2 flow cell and a 100-cycle kit, with read configurations as follows: Read 1 = 50 bp, Read 2 = 72 bp, Index 1 = 8 bp, and Index 2 = 8 bp.
Spatial transcriptomics

treatment_protocol: Muscle injury was induced in young and geriatric C57BL/6J female mice by injecting both TA muscles with 10 μl of notexin. The mice were sacrificed, and TA muscles were collected at 5 dpi.

value: Tibialis Anterior Muscle

value: sex:Female, treatment:10uL Notexin injection and tissue collection 5dpi, age:26 months


title: Young TA Muscle, 5dpi

value: sex:Female, treatment:10uL Notexin injection and tissue collection 5dpi, age:5 months


title: 25-28-H3K27me3-R2


title: C-04-0316

value: European Ancestry

value: Pretreatment


title: 810DNA

value: Dieldrin


title: 25-28-H3K27me3-R1

value: Lung


title: C-11-0287

value: female

value: NPM1c Mutated AML


title: C-02-1744

value: male

value: NPM1c Mutated CN-AML

value: No


title: 809DNA

value: Mouse midbrain

value: Control


title: 25-27N-H3K27me3-R1

value: Non-neoplastic

value: H3K27me3 (Active Motif, #39155)


title: 808DNA

value: Male

value: 36 weeks


title: 25-27N-H3K27me3-R2


title: 25-26N-H3K27me3-R2


title: C-04-1239

value: Bone Marrow

value: NPM1c Mutated Sole Trisomy 8 AML

value: Yes


title: H358 cells, oeEML4, Rep2

city: Toronto

first: Housheng

middle: Hansen

last: He

state: ON

address: 101 College St

country: Canada

institute: UHN

data_processing:
The seuence reads adaptors were trimmed using Cutadapt.
The STAR and HTSeq were employed to align reads to the human genome (hg38) and quantify gene expression levels with annotation GENCODE (version 25)
Assembly: hg38
Supplementary files format and content: Comma-separated values (csv) file includes raw counts for each sample

extract_protocol:
Total RNAs were purified with RNeasy Mini Kit (QIAGEN) or RNAprep Pure Cell/Bacteria Kit (TIANGEN).
Approximately 5 μg of total RNA was used to deplete rRNA using Ribo-Zero Gold rRNA Removal Kit (Illumina). rRNA-depleted RNAs were fragmented using NEBNext® Magnesium RNA Fragmentation Module (NEB) and then reverse-transcribed by SuperScript™ II Reverse Transcriptase (Thermo Fisher Scientific). Next, U-labeled second-stranded DNAs were synthetized with DNA Polymerase I (E. coli) (NEB), RNase H (NEB) and dUTP Solution (Thermo Fisher Scientific). After adding adapters, the fragments were purified with AMPureXP beads, then treated with Uracil-DNA Glycosylase (UDG; NEB) and were amplified by PCR.

tag: cell line

value: non-small cell lung cancer (NSCLC) cell line

value: EML4 overexpression


title: 807DNA


title: 25-26N-H3K27me3-R1

value: Lung


title: H358 cells, oeEML4, Rep1


title: 806DNA

value: Dieldrin


title: 25-25N-H3K27me3-R2


title: 805DNA


title: 804DNA


title: Ox_IP_REP3

city: Cologne

first: Miltos

last: Tsiantis

state: North Rhine-Westphalia

address: Carl-von-Linné-Weg, 10

department: Department of Comparative Development and Genetics

country: Germany

institute: Max Planck Institue for Plant Breeding Research

data_processing:
Quality control, read mapping, and peak calling for the DAP-seq and ChIP-seq analyses were conducted with the ENCODE Uniform processing pipeline for ChIP-seq (https://www.encodeproject.org/chip-seq/transcription_factor/).
Bowtie and MACS2 were selected as mapper and peak caller, respectively, and only IDR-optimal peaks were used.
Peaks were called for case and mock libraries separately, using their respective inputs, and mock peaks were then subtracted from the case peaks using bedtools.
Signal and peak files were visualized and inspected using a local instance of the UCSC genome browser (https://ucscbrowser.mpipz.mpg.de/).
The enriched binding motives were identified by MEME-ChIP (http://meme-suite.org/tools/meme-chip).
Assembly: carhr38
Supplementary files format and content: BigWig files (except for control simples)
Supplementary files format and content: NarrowPeak files (except for control simples)

organism: Cardamine hirsuta

source_name: seedlings

extract_protocol:
The plants grown on soil in short-day conditions were harvested fourteen days after germination. For crosslinking, for each replicate, about 20 g of seedlings (without root and mature leaves) were crosslinked with 1% formaldehyde for 20 min at 4°C.
For sequencing, library construction and subsequent sequencing were performed at the Max Planck-Genome-centre Cologne (https://mpgc.mpipz.mpg.de/home/). The Low input ChIP-seq libraries were constructed using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (E7370).

value: seedlings

value: Oxford

value: GFP antibody ab290


title: 811DNA


title: H358 cells, oeCtrl, Rep1

value: WT


title: 25-25N-H3K27me3-R1


title: 25-24N-H3K27me3-R2


title: H358 cells, siEML4-36, Rep1

value: EML4 knockdown


title: 802DNA

value: Mouse midbrain


title: 25-24N-H3K27me3-R1

value: Non-neoplastic


title: H358 cells, siEML4-36, Rep2


title: Ox_IP_REP1


title: Ox_IP_REP2


title: Ox_input_REP3


title: 803DNA

value: Control


title: H358 cells, siEML4-34, Rep2


title: 800DNA

value: Male


title: Ox_input_REP2


title: 801DNA

value: 36 weeks


title: H358 cells, siEML4-34, Rep1


title: 25-23N-H3K27me3-R1

value: H3K27me3 (Active Motif, #39155)


title: 25-23N-H3K27me3-R2


title: H358 cells, siCtrl, Rep2


title: Ox_input_REP1


title: H358 cells, oeCtrl, Rep2


title: 518DNA1

value: Female


title: ChCUC1V_IP_REP3


title: 25-22N-H3K27me3-R1


title: H358 cells, siCtrl, Rep1


title: 517DNA1


title: 519DNA1


title: A549 cells, siEML4-36, Rep2

value: lung carcinoma epithelial cells


title: ChCUC1V_IP_REP2


title: 25-21N-H3K27me3-R2


title: 516DNA1


title: ChCUC1V_input_REP3


title: 25-21N-H3K27me3-R1


title: ChCUC1V_IP_REP1


title: A549 cells, siEML4-36, Rep1


title: 514DNA1


title: 25-20T-H3K27me3-R2

value: Tumor


title: 515DNA1


title: A549 cells, siEML4-34, Rep1


title: ChCUC1V_input_REP2


title: 25-20T-H3K27me3-R1


title: 25-22N-H3K27me3-R2


title: 513DNA1


title: A549 cells, siEML4-34, Rep2


title: ChCUC1V_input_REP1


title: 25-20N-H3K27me3-R2


title: 511DNA1


title: 25-19T-H3K27me3-R2


title: A549 cells, siCtrl, Rep1


title: 25-20N-H3K27me3-R1


title: halo_REP3

data_processing:
Quality control, read mapping, and peak calling for the DAP-seq and ChIP-seq analyses were conducted with the ENCODE Uniform processing pipeline for ChIP-seq (https://www.encodeproject.org/chip-seq/transcription_factor/).
Bowtie and MACS2 were selected as mapper and peak caller, respectively, and only IDR-optimal peaks were used.
Peaks were called for case and mock libraries separately, using their respective inputs, and mock peaks were then subtracted from the case peaks using bedtools.
Signal and peak files were visualized and inspected using a local instance of the UCSC genome browser (https://ucscbrowser.mpipz.mpg.de/).
The enriched binding motives were identified by MEME-ChIP (http://meme-suite.org/tools/meme-chip).
Assembly: carhr38
Supplementary files format and content: BigWig files (except for control simples)
Supplementary files format and content: NarrowPeak files (except for control simples)
Library strategy: DAP-seq

extract_protocol:
the C. hirsuta genomic DNA was extracted from rosette leaves of 4-week-old plants by Qiagen DNeasy Plant Maxi Kit (Cat No. 68163).
For DNA library preparation, about 5 μg genomic DNA was first sheared by a Bioruptor® Pico sonicator (Diagenode) for 6 cycles (30 sec on/30 sec off) at 4°C to 200-400 bp fragments, followed by end repair, A-tail reaction, and adaptor ligation processes.

tag: dap antibody

value: Magne HaloTag beads


title: halo_REP2


title: 25-19T-H3K27me3-R1

value: Lung


title: halo_REP1


title: 509DNA1


title: ChCUC1_halo_REP3


title: 512DNA1

value: Dieldrin


title: 25-19N-H3K27me3-R2


title: 508DNA1


title: ChCUC1_halo_REP2

value: seedlings


title: 25-19N-H3K27me3-R1


title: 507DNA1


title: 25-18T-H3K27me3-R2


title: A549 cells, siCtrl, Rep2


title: 25-18T-H3K27me3-R1


title: 505DNA1


title: 25-18N-H3K27me3-R2


title: 25-18N-H3K27me3-R1


title: 504DNA1


title: 506DNA1


title: 510DNA1


title: 503DNA1


title: Zp

city: Beijing

first: Yaqing

last: Mao

address: No.22, Zhongguancun South Avenue

country: China

institute: Peking University School and Hospital of Stomatology

data_processing:
Genome mapping was performed on the preprocessed reads using the spliced mapping algorithm Hisat2 (version:2.0.4) with default parameters.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Reads were converted into FPKM (Fragments Per Kilobase of exon model per Million mapped reads) to standardize the amount of gene expression
Stringtie (version:1.3.0) was applied to count the number of Fragments for each gene after Hisat2 comparison, and then TMM (trimmed mean of M values) was used for normalization. Perl script was used to calculate the FPKM value for each gene.
Assembly: GRCh38
Supplementary files format and content: xls file includes raw counts and FPKM values for each Sample

source_name: cell line

growth_protocol: Cells were grown in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) containing 10% fetal bovine serum (FBS, Gibco) and antibiotics (streptomycin and penicillin, Gibco) at 37 °C in a 5% CO2 humidified incubator.

extract_protocol:
Total RNA was extracted using PAXgene Blood miRNA Kit (Cat# 763134, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 4200 TapeStation (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
The library was constructed using a VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme; Cat#NR604-02).

treatment_protocol: ZNF582 overexpression plasmids were transfected into HN6 by using polybrene (Solarbio, Beijing, China; Cat#H8761)

value: cell line

value: Human tongue squamous cell carcinoma

value: ZNF582 overexpression

value: ZNF582 overexpressed


title: Np

value: WT


title: 25-17T-H3K27me3-R2


title: 502DNA1

value: Mouse midbrain


title: A549 cells, RIP-seq, FTO_IP

description:
raw_counts.csv
m6A_regulators_RIP-seq_targets.xlsx

data_processing:
The sequence reads adaptors were trimmed using Cutadapt.
The STAR and HTSeq were employed to align reads to the human genome (hg38) and quantify gene expression levels with annotation GENCODE (version 25). Then, the DESeq2 was applied for normaliztion and caculating Fragments Per Kilobase Million (FPKM). Lastly, the target genes bound by m6A regulators were defined as genes with FPKM of INPUT greater than 1 and enrichment fold change (IP FPKM/INPUT FPKM) greater than 1.5
Assembly: hg38
Supplementary files format and content: Comma-separated values (csv) file includes raw counts for each sample
Supplementary files format and content: xlsx file includes the RIP-seq based m6A regulators target gene lists

extract_protocol:
RIP was performed using Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (MilliporeSigma) with some modifications. A549 cells were harvested for each IP reaction and lysed in Complete RIP Lysis Buffer. 5% of the volume of cell lysate was saved as INPUT, mixed with 350 μl TRIzol. 50 μl of protein A/G magnetic beads were washed by RIP Wash Buffer, resuspended in 100 μl of RIP Wash Buffer containing 5 μg anti-METTL3 antibody  (Abcam),  anti-ALKBH5 antibody (Proteintech), anti-WTAP antibody (Abcam), anti-METTL14 antibody (Cell Signaling Technology) and anti-FTO antibody (Proteintech) at 4°C overnight, respectively. The antibody-bead mixture was washed and resuspended in 900 μl of RIP Immunoprecipitation Buffer and 100 μl of cell lysate and incubated for 4 h at 4°C. The beads were then washed 5 times and re-suspended with 350 μl TRIzol as IP. RNAs from INPUT and IP were extracted using RNeasy Mini Kit (QIAGEN).
Library construction was conducted using SMARTer Stranded Total RNA-Seq Kit version 2-Pico Input Mammalian (Takara/Clontech).

tag: rip antibody

value: anti-FTO antibody (Cat. #27226-1-AP, Proteintech)


title: 25-17N-H3K27me3-R2

value: Non-neoplastic


title: ChCUC1_halo_REP1

value: Oxford


title: 500DNA1

value: 36 weeks


title: A549 cells, RIP-seq, ALKBH5_IP

value: anti-ALKBH5 antibody (Cat. #16837-1-AP, Proteintech)


title: PerM, WT control

type: RNA

city: Manhasset

first: Atsushi

last: Murao

address: 350 Community Dr

institute: The Feinstein Institutes for Medical Research

description:
Control
SAMPLE 1

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/us/analyze.  Target gene signals normalized to house keeping gene ACTB
Fold Change worksheet reports test/control (i.e., rmCIRP/PBS) ratios.

label: SYBR Green

source_name: Peritoneal macrophages

label_protocol: PCR assay were performed using mouse circadian rhythms PCR array (Qiagen, Germantown, MD) following the Manufacture's instructions

growth_protocol: PerM was cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum (FBS), 2 mM glutamine, 100 IU/ml penicillin‒streptomycin, and 25 mM HEPES at 37 °C in 5% CO2

extract_protocol: Total RNA was extracted with RNAspin Mini kit with DNase 1 treatment

treatment_protocol: Cells were treated with 1ug/ml rmCIRP for 24 h prior to to gene expression analysis

value: Peritoneal macrophages

value: control


title: 25-17N-H3K27me3-R1

value: H3K27me3 (Active Motif, #39155)


title: A549 cells, RIP-seq, WTAP_IP

value: anti-WTAP antibody (Cat. #ab195380, Abcam)

value: lung carcinoma epithelial cells


title: 719DNA

value: Male

value: 12 weeks

value: Control


title: PerM, TREM-1-/- rmCIRP treatment

description:
Test
SAMPLE 4

value: rmCIRP


title: PerM, WT rmCIRP treatment

description:
Test
SAMPLE 2


title: 25-16T-H3K27me3-R2

value: Lung

value: Tumor


title: PerM, TREM-1-/- control

description:
Control
SAMPLE 3


title: 25-16T-H3K27me3-R1


title: A549 cells, RIP-seq, METTL14_IP

value: anti-METTL14 antibody (Cat. #48699, Cell Signaling Technology)

value: WT


title: 716DNA

value: Mouse midbrain

value: Dieldrin


title: Lycium chinense Mill, fruit

city: Nanjing

first: Xiaozhu

last: Tang

address: Xianlin Road

institute: Nanjing University of Chinese University

description: Lycium chinense Mill

data_processing:
150 bp paired-end reads were mapped to the reference Lycium chinense Mill by using Bowtie2.  Genome build used for read alignment for Lycium_chinense_Mill.bam and mice_blood.bam was Lycium barbarum chloroplast, complete genome NCBI Reference Sequence: NC_041110.1.  https://www.ncbi.nlm.nih.gov/nuccore/NC_041110.1
Only unique mapping paired reads were sorted using SAMtools and kept for subsequent analysis.
Fastp 0.19.11 software performs basic quality statistics for raw reads. QC analysis was used by fastqc v0.11.5. Burrows Wheeler aligner(0.7.12-r1039) can compare reads to reference genome. Peak calling was performed by MACS22.1.0. The motifs were recognized by Homer findMotifsGenome.pl(v4.9.1).
The file type of mice_blood_peaks_table.tsv was peak file.
Assembly: NC_041110.1
Supplementary files format and content: Peaks file mice_blood_peaks_table.tsv

organism: Lycium chinense

source_name: fruit

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: we intragastric gavaged C57 BL/6J mice with Lycium chinense Mill at a dose of 10 mL/kg. After 14 days, the blood was drawn and subjected to Illumina deep-sequencing technology

value: fruit


title: SW1990_Clone 4_G12D/K128R

city: Leuven

first: Wout

last: Magits

address: Herestraat 49, bus 912

country: Belgium

institute: VIB-KULeuven Center for Cancer Biology

data_processing:
Reads were mapped on GRCh38 human transcriptome reference with HISAT2.
Read counts were normalized by calculating FPKM
Assembly: Hg38
Supplementary files format and content: txt file containing  fpkm values for each sample

extract_protocol:
Cells were trypsinized, peletted, and RNA was harvested using Nucleospin tissue kit (Macherey).
mRNA library preparation (poly A enrichment)

value: KRAS G12D/K128R


title: SW1990_Clone 4_G12D

value: KRAS G12D


title: SW1990_Clone 5_G12D


title: SW1990_Clone 5_G12D/K128R


title: SW1990_Clone 3_G12D/K128R


title: A549 cells, RIP-seq, METTL3_IP

value: anti-METTL3 antibody (Cat. #ab195352, Abcam)


title: 25-16N-H3K27me3-R2

value: Non-neoplastic

value: H3K27me3 (Active Motif, #39155)


title: 717DNA


title: 25-17T-H3K27me3-R1


title: 715DNA


title: A549 cells, RIP-seq, INPUT

value: lung carcinoma epithelial cells


title: SW1990_Clone 3_G12D


title: 25-16N-H3K27me3-R1


title: 714DNA

value: Male


title: wt_elf1Y99A_uv2hr_A3

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

data_processing:
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using A1-A6 barcodes, and the barcode sequences were trimmed, as well as the 3' nucleotide of the sequencing read, using a custom perl script
Fastq files were aligned to the yeast genome (SacCer3 or SacCer3+pUC19) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to dipyrimidine sequences (i.e., TT, TC, CT, CC), corresponding to CPD lesions were retained in BED file using custom perl script.
BED files were converted to WIG file using COUNT function of IGVTools
Background values dipyrimidine sequences were generated in WIG file using custom perl script
Assembly: SacCer3
Supplementary files format and content: WIG files containing counts of DNA CPD lesion reads filtered for only dipyrimidine mapping sequences and including background value of 0.0 at nucleotides associated with dipyrimidines with no mapped sequencing reads. A sequencing read count was assigned to each nucleotide in the lesion-containing dipyrimidine sequence. For no UV (untreated samples), just a txt file with dinucleotide counts are provided

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Yeast cultures containing the indicated mutants were grown in YPD (yeast extract, peptone, dextrose) to OD600=~0.8 in a yeast shaker.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with 250 μl of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA), 250 μl of PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and 150 μl of acid-washed glass beads, and vortexed vigorously twice, 2 min each time. After adding 200 μl of TE (10mM Tris-HCl, pH 7.5, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 1 ml of ethanol to precipitate DNA at room temperature for 5 min. DNA pellet was dissolved in 200 μl of TE and incubated with 2 μl of RNase A/T1 (ThermoFisher Scientific) at 37˚C for 1 hr to remove RNA. DNA was subsequently purified with PCI extraction, ethanol precipitated, and disolved in sterile deionized H2O. The purified genomic DNA was quantified and 5 μg of DNA was used for each sequencing library preparation.
CPD-seq procedure is adopted from the published emRiboSeq method (Nature Protocols 2015 10, 1433–1444). Briefly, DNA fragments were first ligated to a double-stranded adaptor DNA trP1, and free 3'-OHs were blocked by terminal transferase and dideoxy-ATP.  CPD lesions were  cleaved with T4 endonuclease V and apurinic/apyrimidinic (AP) endonuclease, APE 1, to generage new 3'-OHs. DNA was then ligated to adaptor  A. Up to 6 different barcoded A adaptors (A1: AAGAGGAT; A2: TTCGTGAT; A3: CCTGAGAT A4: ATCGCGAT; A5: TACTGGAT; and A6: GAACTGAT) were used to generate libraries for different experiments. DNA was purified with Streptavidin beads and amplified for up to 6 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing.
OTHER (CPD-seq)

treatment_protocol: Yeast cells were harvested and resuspended in sterile deionized H2O and irradiated with 125 J/m2 UVC. Following UV irradiation, cells were spun down and resuspended in pre-warm YPD medium (yeast extract, peptone, dextrose) to allow for repair. Aliquots (10 ml of yeast culture) were taken before UV irradiation (No UV), immediately after UV irradiation (0hr), and at 2 hours after UV irradiation (2hr). Cells were spun down and stored at -80˚C until genomic DNA isolation.

value: Yeast cells

value: UV irradiated 125 J/m2

tag: repair time

value: 2 hr


title: 713DNA

value: 12 weeks

value: Control


title: DISCOVER-seq control 12h HEK293T 5000k

first: Xun

last: Lan

address: Haidian District

department: School of Medicine

institute: Tsinghua University

data_processing:
For Tracking-seq, please refer to https://github.com/Lan-lab/offtracker.
For other data, fastq files were mapped to mm10 using bowtie2. SAM files were converted to BAM files with samtools. BAM files were converted to bedgraph files by deeptools and then converted to bigwig files with bedGraphToBigWig after normalization
Assembly: hg38 or mm10
Supplementary files format and content: BigWig of sequencing signals

extract_protocol:
Cells were crosslinked with 1% formaldehyde. After quenching and blocking the beads, MRE11 or H3K4me3 antibody were added. After cell lysis, the lysate was sonicated using a QSONICA sonicator with microtips. DNA was then treated with RNase A and Proteinase K, followed by purification through phenol-chloroform extraction.
The libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit.
For Tracking-seq, cells were fixed with Concanavalin A bead, washed, and resuspended with buffer containing RPA2/IgG antibodies. pA-MNase was added to cleavage the DNA. Cleavaged fragments were collected and then digested with DNase. For Tracking-seq, DNA was purified with DNA Clean Beads and then HL-dsDNase was added to remove dsDNA.  For ChIP-seq, Cells were crosslinked with 1% formaldehyde. After quenching and blocking the beads, MRE11 or H3K4me3 antibody were added. After cell lysis, the lysate was sonicated using a QSONICA sonicator with microtips. DNA was then treated with RNase A and Proteinase K, followed by purification through phenol-chloroform extraction. For ATAC-seq, 100,000 NIH3T3 cells, AML12 cells, mHSPCs, or mESCs were sorted into tube for tagmentation and purifcation.
The strand-specific ssDNA libraries were constructed using VAHTS ssDNA Library Prep Kit. Other libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit.


title: wt_elf1Y99A_uv0hr_A2

value: 0 hr


title: 712DNA


title: 25-15T-H3K27me3-R1

value: Lung

value: Tumor


title: DISCOVER-seq-plus Cas9 VEGFA2 12h HEK293T 5000k


title: 25-15N-H3K27me3-R2


title: DISCOVER-seq-plus Cas9 HEK4 12h HEK293T 5000k


title: 711DNA

value: Mouse midbrain


title: 25-15N-H3K27me3-R1


title: rad26_elf1Y99A_uv2hr_A6

value: rad26-delta elf1-Y99A


title: rad26elf1cdel_uv0hr_A4

value: rad26-delta elf1-CTD-delta


title: 25-14T-H3K27me3-R1


title: 710DNA

value: Dieldrin


title: rad26elf1cdel_uv2hr_A5


title: DISCOVER-seq Cas9 VEGFA2 12h HEK293T 5000k


title: DISCOVER-seq Cas9 HEK4 24h HEK293T 5000k


title: 25-14N-H3K27me3-R2


title: DISCOVER-seq Cas9 HEK4 12h HEK293T 5000k


title: CUT&RUN MRE11 Cas9 HEK4 12h HEK293T 500k rep1

data_processing:
For Tracking-seq, please refer to https://github.com/Lan-lab/offtracker.
For other data, fastq files were mapped to mm10 using bowtie2. SAM files were converted to BAM files with samtools. BAM files were converted to bedgraph files by deeptools and then converted to bigwig files with bedGraphToBigWig after normalization
Assembly: hg38 or mm10
Supplementary files format and content: BigWig of sequencing signals
Library strategy: Cut & Run

extract_protocol:
Cells were fixed with Concanavalin A bead, washed, and resuspended with buffer containing RPA2/MRE11/IgG antibodies. pA-MNase was added to cleavage the DNA. Cleavaged fragments were collected and then digested with DNase. For Tracking-seq, DNA was purified with DNA Clean Beads and then HL-dsDNase was added to remove dsDNA.
The strand-specific ssDNA libraries were constructed using VAHTS ssDNA Library Prep Kit. CUT&RUN-MRE11 library was constructed using NEBNext® Ultra™ II DNA Library Prep Kit.
For Tracking-seq, cells were fixed with Concanavalin A bead, washed, and resuspended with buffer containing RPA2/IgG antibodies. pA-MNase was added to cleavage the DNA. Cleavaged fragments were collected and then digested with DNase. For Tracking-seq, DNA was purified with DNA Clean Beads and then HL-dsDNase was added to remove dsDNA.  For ChIP-seq, Cells were crosslinked with 1% formaldehyde. After quenching and blocking the beads, MRE11 or H3K4me3 antibody were added. After cell lysis, the lysate was sonicated using a QSONICA sonicator with microtips. DNA was then treated with RNase A and Proteinase K, followed by purification through phenol-chloroform extraction. For ATAC-seq, 100,000 NIH3T3 cells, AML12 cells, mHSPCs, or mESCs were sorted into tube for tagmentation and purifcation.
The strand-specific ssDNA libraries were constructed using VAHTS ssDNA Library Prep Kit. Other libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit.


title: 709DNA


title: 708DNA


title: 707DNA


title: rad16elf1cdel_uv2hr_A5

value: rad16-delta elf1-CTD-delta


title: 501DNA1

value: Female

value: 36 weeks


title: 25-15T-H3K27me3-R2

value: H3K27me3 (Active Motif, #39155)


title: 25-14N-H3K27me3-R1

value: Non-neoplastic


title: wt_elf1Y99A_nouv_A1

value: Yeast cells


title: WT HEK293T 500k RPA2 rep1

data_processing:
For Tracking-seq, please refer to https://github.com/Lan-lab/offtracker.
For other data, fastq files were mapped to mm10 using bowtie2. SAM files were converted to BAM files with samtools. BAM files were converted to bedgraph files by deeptools and then converted to bigwig files with bedGraphToBigWig after normalization
Assembly: hg38 or mm10
Supplementary files format and content: BigWig of sequencing signals
Library strategy: Track-seq


title: 25-13T-H3K27me3-R2

data_processing:
Raw ChIP-seq reads were aligned to hg19 genome by bwa (0.7.17).
Aligned reads were deduplicated and those with MAPQ>=10 were retained.
Narrow peaks (H3K27ac, H3K4me1, H3K4me3) were called by MACS2 (2.2.7.1) with q-value<=0.05. Board peaks (H3K27me3, H3K9me3) were called by Homer findPeaks in histone mode with p-value<=0.05.
Raw RNA-seq reads were trimmed by Trim Galore.
Trimmed RNA-seq reads were aligned to hg19 genome by STAR.
Assembly: hg19
Supplementary files format and content: bigwig track files (ChIP-seq)
Supplementary files format and content: txt gene read count files (RNA-seq)


title: rad16elf1cdel_uv0hr_A4

value: UV irradiated 125 J/m2


title: WT HEK293T 500k IgG rep1


title: WT HEK293T 100k RPA2 rep1


title: rad16elf1cdel_noUV_A6


title: 705DNA

value: Male


title: 704DNA

value: 12 weeks


title: elf1cdel_uv2hr_A3

value: 2 hr


title: PE3 VEGFA2 72h HEK293T 400k PEI rep1


title: 25-13N-H3K27me3-R1


title: elf1cdel_uv0hr_A2

value: 0 hr


title: PE3 VEGFA2 24h HEK293T 400k PEI rep1


title: rad26_elf1Y99A_uv0hr_A5


title: 25-12-H3K27me3-R2

value: Lung


title: PE3 VEGFA2 48h HEK293T 400k PEI rep1


title: 25-13N-H3K27me3-R2


title: 701DNA

value: Control


title: 703DNA

value: Mouse midbrain


title: 702DNA


title: PE3 VEGFA2 12h HEK293T 400k PEI rep1


title: 706DNA


title: 700DNA


title: PE2 VEGFA2 48h HEK293T 200k PEI rep2


title: 25-10-H3K27me3-R2


title: 25-13T-H3K27me3-R1

value: Tumor


title: 417DNA

description: Sample 417 incorrectly labeled as 718 during sample submission, explaining the different naming in sequencing files.


title: PE2 VEGFA2 48h HEK293T 200k PEI rep1


title: 25-10-H3K27me3-R1


title: 416DNA


title: elf1cdel_nouv_A1


title: 25-9-H3K27ac-R2


title: PE2 VEGFA2 24h HEK293T 200k PEI rep2


title: 25-9-H3K27ac-R1


title: 415DNA


title: 414DNA


title: PE2 HEK4 72h HEK293T 500k PEI rep1


title: 25-12-H3K27me3-R1


title: PE2 VEGFA2 24h HEK293T 200k PEI rep1


title: 25-8-H3K27ac-R2


title: 413DNA


title: PF_NF54_tdTomato-peg4, scRNAseq [SI-GA-C1_4]

city: Stockholm

first: Mubasher

last: Mohammed

state: Stockholm lan

address: Svante Arrhenius Väg 20c, MBW, Stockholms University

department: Department of Molecular Biosciences, the Wenner-Gren Institute

country: Sweden

institute: Stockholm University

description:
SMART-seq2
200922_A00181_0206_AHT2VJDRXX

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cellranger (version 5.0.1)
Assembly: reference genome of Plasmodium falciparum version 50 (ASM276v2)
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Tab-seprated cells barcodes and metadata

organism: Plasmodium falciparum

source_name: P. falciparum NF54-tdTomato

extract_protocol:
Gametocyte cells were converted to barcoded scRNA-seq libraries using Chromium Single Cell 3′ reagent kits (V3) (10X Genomics) according to the manufacturer’s instructions (CG000183 Rev A), aiming for 4,000–8,000 cells per library. Library quality control and quantification were performed using a KAPA Library Quantification kit for Illumina platforms (Kapa Biosystems, Cape town; South Africa) and a 2100 Bioanalyzer High Sensitivity DNA kit (Agilent, Santa Clara; US). Libraries were sequenced in an Illumina HiSeq 2500 on Rapid Run settings using asymmetric paired-end sequencing (26 cycles for Read 1 and 98 cycles for Read 2) pair-ended 150 bp (PE 150) reads that yielded approximately 160 million reads per run.
Chromium Single Cell 3′ reagent kits (V3) 10XGenomics

value: P. falciparum NF54-tdTomato

value: pfalciparum 3D7


title: PE2 HEK4 48h HEK293T 500k PEI rep1


title: 25-8-H3K27ac-R1

extract_protocol:
Nuclei extraction: Samples were shipped to Virginia Tech on dry ice and stored in liquid nitrogen vapor phase until use. Thin slices were cut from the tissue on dry ice with a sharp scalpel and transferred to the grinder (D9063, Sigma-Aldrich) pre-cooled on ice. Subsequent steps were performed on ice and centrifugation performed at 4°C. 3 ml of ice-cold nuclei extraction buffer [0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM tris-HCl, and 0.1% Triton X-100, with 30 µl of PIC (P8340, Sigma-Aldrich), 3 µl of 100 mM PMSF, and 3 µl of 1 M dithiothreitol added before use] was added to the grinder. Tissue was homogenized by slowly douncing 20 times with pestle A and 30 times with pestle B. Homogenate was filtered through a 40 µm cell strainer into a 15 ml tube and centrifuged at 1000g for 10 min. Supernatant was removed and the crude nuclei pellet was resuspended in 500 µl nuclei extraction buffer and transferred to a 1.5 ml tube. 750 µl of 50% iodixanol, 7.5 µl of PIC, 0.75 µl of 100 mM PMSF and 0.75 µl of 1M dithiothreitol were added and mixed by gently pipetting and then inverting the tube five times. The mixture was centrifuged at 10,000g for 20 min and the supernatant was removed. The purified nuclei pellet was resuspended in 200 µl of Dulbecco's phosphate-buffered saline (DPBS).  MNase digestion of chromatin: Resuspended nuclei were counted and diluted to 4×10^6/ml if needed. 2 µl of PIC, 2 µl of 100 mM PMSF and 200 µl lysis buffer [4% Triton X-100, 100 mM tris-HCl, 100 mM NaCl, and 30 mM MgCl2] were added to 200 µl of nuclei suspension, mixed by vortexing and incubated at room temperature for 10 min. 20 µl of 100 mM CaCl2 and 5 µl of 100U MNase (88216, Thermo Fisher Scientific) were added, mixed by vortexing and incubated at room temperature for 10 min. 44 µl of 0.5 M EDTA was then added, mixed by vortexing and incubated on ice for 10 min. The solution was centrifuged at 16,100g for 5 min at 4°C. Supernatant containing chromatin fragments were transferred to a new 1.5 ml tube and placed on ice. 30 µl of chromatin solution was used for each ChIP assay (~50K nuclei).  Preparation of immunoprecipitation beads: 5 µl of protein A Dynabeads (10001D, Invitrogen) were used in each MOWChIP assay. The beads were washed twice with IP buffer (20 mM tris-HCl, pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% (w/v) sodium deoxycholate, 0.1% SDS, 1% (v/v) Triton X-100) and resuspended in 150 µl of IP buffer. The following antibodies were used in this work: anti-H3K27ac (ab4729, Abcam), 0.125 µg/assay; anti-H3K4me1 (39297, Active Motif), 0.5 µl/assay; anti-H3K4me3 (ab8580, Abcam), 0.125 µg/assay; anti-H3K27me3 (39155, Active Motif), 0.5 µg/assay; anti-H3K9me3 (ab8898, Abcam), 0.125 µg/assay. The suspension was incubated on a rotator at 4°C overnight. The beads were washed with IP buffer twice and resuspended in 5 µl of IP buffer for loading in the MOWChIP device.  MOWChIP: The microfluidics based MOWChIP process, including device fabrication and operation, was performed following our published protocol (Zhu, B., Hsieh, YP., Murphy, T.W. et al. MOWChIP-seq for low-input and multiplexed profiling of genome-wide histone modifications. Nat Protoc 14, 3366–3394 (2019).).  RNA extraction: Tissue slices were placed in 200 µl of RNAlater-ICE frozen tissue transition solution (AM7030, Thermo Fisher Scientific) prechilled to -80°C. They were then incubated at -20°C overnight. Each RNA-seq library was prepared from 10ng RNA extracted from the tissue. Two technical replicates were prepared for each sample. Total RNA was extracted from the incubated tissue using the RNeasy Mini Kit (74104, Qiagen) and RNase-Free DNase Set (79254, Qiagen).
ChIP-seq: Libraries were prepared using 2S Plus DNA library kit (IDT) following the manufacturer’s protocol. 1 × EvaGreen dye (Biotium) was added to the qPCR amplification mixture to monitor progress of amplification. Library was eluted to 7 µl of low EDTA TE buffer. Library size distribution was examined using TapeStation (Agilent) and concentration was quantified with Kapa Library Quantification kit (Kapa Biosystems).  RNA-seq: Extracted total RNA was resuspended in 4.5 μL of RNase-free water with 5% RNase inhibitor (40 U/μL) added. 2 μL of oligo-dT primer (10 μM), 2 μL of dNTP mix (10 mM) and 4.3 μL of total RNA solution were mixed, incubated at 72°C for 3 minutes and immediately put on ice. Then 1 μL of SuperScript II reverse transcriptase (200 U/μL), 0.5μL of RNase inhibitor (40 U/μl), 4μL of Superscript II first-strand buffer, 1 μL of DTT (100 mM), 4 μL of 5 M Betaine, 0.12 μL of 1 M MgCl2, 0.2 μL of TSO (100 μM), 0.88 μL of nuclease-free water were added to the 8.3 μl mixture mentioned above. The reverse transcription (RT) reaction mix was then incubated at 42°C for 90 minutes, followed by 10 cycles of 50°C for 2 minutes and 42°C for 2 minutes, and lastly 70°C for 15 minutes. The RT reaction mix was mixed with 25 μL KAPA HiFi HotStart ReadyMix, 0.5 μL IS PCR primers (10 μM), 2.5 μL Evagreen dye, and 2 μL nuclease-free water, and amplified with: 98°C for 1 minute, 9–11 cycles of 98°C 15 seconds, 67°C 30 seconds, 72°C 6 minutes. The cDNA was purified using 30 μL of SPRIselect beads and eluted in 5 μL of low EDTA TE buffer. The RNA-seq library was made using tagmentation. 3 μL of home-made Tn5 was mixed with 3 μL of 50 μM pre-annealed P5/P7 transposon and incubated at 37°C for 1 hour. Assembled P5 and P7 transposons were then mixed well to form Tn5 mix. 1 μL cDNA (600 pg) and 1 μL of tagmentation buffer (TNP92110, Lucigen) were added to 8 μL Tn5 mix, and the mixture was incubated at 37°C for 1 hour. 1 μL of 10X stop buffer (TNP92110, Lucigen) was then added to the mixture to quench tagmentation. 11 μL SPRIselect beads were used to purify tagmented cDNA. The cDNA was then eluted in 9.5 μL of low EDTA TE buffer. 25 μL of KAPA HiFi HotStart ReadyMix was incubated at 98°C for 30 seconds, mixed with 9.5 μL tagmented cDNA and incubated at 72°C for 5 minutes. 1.5 μL of 100 μM P5 primer, 1.5 μL of 100 μM P7 primer, 10 μL nuclease-free water and 2.5 μL Evagreen were then added and amplified with: 98°C for 30 seconds; 10-12 cycles of 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 30 seconds. Amplified cDNA libraries were purified with 50 μL SPRIselect beads and eluted in 8 μL of low EDTA TE buffer. The RNA library preparation is adapted from Smart-Seq2 workflow (Picelli, S., Faridani, O., Björklund, Å. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 9, 171–181 (2014).)


title: 412DNA

data_processing:
Adapter trimming: Read adapters were trimmed using the trim_galore tool (version 0.4.5). In trim_galore, we used the default minimum quality score and added a stringency value of 6, thereby requiring a minimum overlap of 6 bp.
Read alignment: Reads were aligned to the mm10 genome using bismark (version 0.19.1) and bowtie2 (version 2.3.2) with default parameters.
Coverage file generation: Methylation data was extracted from the aligned reads in bismark (version 0.19.1) using a minimum threshold of 5 reads to include a CpG site in analysis.
Assembly: mm10
Supplementary files format and content: Bismark coverage files (.cov.gz) contain % methylation beta values for CpG sites with sequencing coverage.

value: Dieldrin


title: BEAS-2B cells, control

city: Ilsandong-gu, Goyang-si

first: Dong-Hee

last: Han

state: Gyeonggi-do

address: 32, Dongguk-ro

department: Life science

country: South Korea

institute: Dongguk University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Bronchus

growth_protocol: A549, BEAS-2B cells were maintained in RPMI1640 medium supplemented with 10% fetal bovine serum, 1% antibiotics, and 1% sodium pyruvate in a humidified atmosphere at 5% CO2 and 37°C.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

treatment_protocol: 24 hours after cell seeding, cells were treated with 1 and 5 ng/mL of TGF-β1 along with RPMI1640 medium containing 1% FBS, fetal bovine serum, 1% antibiotics, and 1% sodium pyruvate. TGF-β1 treatment was carried out for 48 hours.

value: Bronchus

value: Bronchial epithelial cells

value: WT


title: BEAS-2B cells, 1 ng/mL of TGF-β1

value: 1 ng/mL of TGF-[beta]1


title: A549 cells, 1 ng/mL of TGF-β1

value: Lung carcinoma epithelial cells


title: A549 cells, control


title: PF_NF54_tdTomato-peg4, scRNAseq [SI-GA-C1_3]


title: A549 cells, 5 ng/mL of TGF-β1

value: 5 ng/mL of TGF-[beta]1


title: BEAS-2B cells, 5 ng/mL of TGF-β1


title: 25-7-H3K27ac-R2

value: Non-neoplastic


title: PE2 HEK4 48h HEK293T 500k PEI rep1-2


title: PF_NF54_tdTomato-peg4, scRNAseq [SI-GA-C1_2]


title: 411DNA

extract_protocol:
DNA was isolated from tissue punches using Qiagen QIAamp DNA Micro Kits (Qiagen, Cat. # 56304) according to manufacturer instructions for Isolation of Genomic DNA from Tissues with the following modifications and optional steps included to increase yield. Prior to addition of ATL buffer to punches, 80 µL PBS was added and a 1.5 mL tube pestle was used to manually homogenize the sample. 100 µL ATL buffer was added to each sample. For the proteinase K digestion step, samples were incubated at 56°C overnight. Carrier RNA was added to Buffer AL. The incubation time after addition of 100% EtOH was increased to 10 minutes. The incubation time for the elution step was increased to 5 minutes and this step was repeated a second time. DNA was eluted in 54 µL of 10 mM Tris-HCl, pH 8.0.
SeqCap Epi custom bait probes for regions of interest were designed using the Roche NimbleDesign software.Capture hybridization-sequencing libraries were prepared by the Van Andel Institute Genomics Core from 100 ng of high molecular weight DNA using the Accel-NGS Methyl-Seq DNA Library kit (v3.0) (Swift Biosciences, Cat. #30024). DNA was sheared following manufacturer’s protocol to an average size of 250bp, and sheared DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (Zymo Research, Cat. #D5005) with an elution volume of 15 µL. Following adapter ligation, 8 cycles of library amplification were performed. Amplified libraries were pooled in batches of 8 and targeted enrichment of our custom regions was performed using Roche SeqCap Epi developer probes (Supplementary File 1) and SeqCap HyperEpi workflow starting at step 4.0 with the following modifications. The capture was performed using IDT xGen Universal blockers to replace the SeqCap HE Universal Oligo and SeqCap HE Index Oligo. The post-capture amplification was also adjusted to 11 cycles of amplification and the final extension changed from 30 seconds to 1 minute. Quality and quantity of the finished library pools were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.) and QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA. Sequencing (100 bp, paired end) was performed on an Illumina NovaSeq6000 sequencer using an S4, 200 bp sequencing kit (Illumina Inc., San Diego, CA, USA) with 10% PhiX included to improve base diversity. Base calling was done by Illumina Real Time Analysis 3 and output of NextSeq Control Software was demultiplexed and converted to FastQ format with the Illumina Bcl2fastq software (version 1.9.0).
Capture hybridization sequencing (targeted bisulfite-seq)

value: Female

value: 12 weeks


title: PE2 HEK4 24h HEK293T 500k PEI rep2


title: 25-7-H3K27ac-R1


title: 410DNA


title: PF_NF54_tdTomato-peg4, scRNAseq [SI-GA-C1_1]


title: PE2 HEK4 24h HEK293T 500k PEI rep1


title: 25-6-H3K27ac-R2


title: 409DNA


title: 25-6-H3K27ac-R1


title: PE2 HEK4 24h HEK293T 500k PEI rep1-2


title: 25-5-H3K27ac-R1


title: 408DNA


title: 25-5-H3K27ac-R2


title: PE2 HEK4 12h HEK293T 500k PEI rep1


title: PF_NF54_tdTomato-peg4, scRNAseq [SI-GA-B1_3]


title: PF_NF54_tdTomato-peg4, scRNAseq [SI-GA-B1_2]


title: 407DNA


title: PF_NF54_tdTomato-peg4, scRNAseq [SI-GA-B1_1]


title: 405DNA


title: HU WT HEK293T 500k IgG rep1


title: 404DNA


title: 25-4-H3K27ac-R1


title: HU WT HEK293T 500k RPA2 rep1


title: CMN_09

city: Zurich

first: Enni

last: Markkanen

address: Winterthurerstr. 260

institute: University of Zurich

description: 100 bp

data_processing:
Read abundance quantification using Kallisto pseudoalignment - reference CanFam3.1
Transcripts summarised at gene level using tximport
Assembly: CanFam3.1
Supplementary files format and content: Raw counts matrix summarised at gene level

organism: Canis lupus familiaris

source_name: mNormal

extract_protocol:
Covaris truXTRAC® FFPE RNA kit
SMARTer Stranded Total RNA-Seq Kit – Pico Input Mammalian (Takara Bio)

value: mNormal

value: Mucosal

value: Stromal tissue


title: Cas9 tru-VEGFA3 96h HEK293T 500k PEI rep2


title: 25-34-H3K27ac-R2

value: Lung


title: PF_NF54_tdTomato-peg4, scRNAseq [SI-GA-B1_4]


title: Cas9 tru-VEGFA3 96h HEK293T 500k PEI rep1


title: 25-34-H3K27ac-R1

value: Tumor


title: 402DNA

value: Mouse midbrain


title: CMN_07

description: 100 bp


title: HU WT HEK293T 500k RPA2 rep2


title: Cas9 tru-VEGFA1 96h HEK293T 500k PEI rep2


title: 25-4-H3K27ac-R2


title: 25-33-H3K27ac-R2


title: 401DNA

value: Control


title: CMN_06

description: 100 bp


title: Cas9 tru-VEGFA1 96h HEK293T 500k PEI rep1


title: CMN_05

description: 100 bp


title: CMN_04

description: 100 bp


title: 400DNA

value: Dieldrin


title: Cas9 VEGFA3 96h HEK293T 500k PEI rep2


title: 25-33-H3K27ac-R1


title: CMN_08

description: 100 bp


title: 619DNA1

value: Male

value: 6 weeks


title: CMN_03

description: 100 bp


title: Cas9 VEGFA3 96h HEK293T 500k PEI rep1


title: 618DNA1


title: 403DNA


title: CMN_02

description: 100 bp


title: Cas9 VEGFA2 96h HEK293T 500k PEI rep1


title: 25-32-H3K27ac-R1


title: 406DNA


title: 617DNA1


title: CMN_01

description: 100 bp


title: Cas9 VEGFA2 72h HEK293T 500k PEI rep1


title: 616DNA1


title: 25-31-H3K27ac-R1


title: 25-30-H3K27ac-R2


title: Cas9 VEGFA2 48h HEK293T 5k PEI rep1


title: 25-30-H3K27ac-R1


title: CMM_20

description: 100 bp

source_name: mCAS

value: mCAS


title: 615DNA1


title: 614DNA1


title: 25-29-H3K27ac-R2


title: CMM_19

description: 100 bp


title: Cas9 VEGFA2 48h HEK293T 500k PEI-RPA3 rep1


title: CMM_18

description: 100 bp


title: 612DNA1


title: Cas9 VEGFA2 48h HEK293T 500k PEI-RPA1 rep1


title: 25-29-H3K27ac-R1


title: CMM_21

description: 100 bp


title: 25-31-H3K27ac-R2


title: 25-28-H3K27ac-R2


title: CMM_17

description: 100 bp


title: CMM_16

description: 100 bp


title: 25-28-H3K27ac-R1


title: 611DNA1


title: 25-14T-H3K27me3-R2

value: H3K27me3 (Active Motif, #39155)


title: CMM_15

description: 100 bp


title: 610DNA1


title: Cas9 VEGFA2 48h HEK293T 500k ELEC rep1


title: Cas9 VEGFA2 48h HEK293T 500k ELEC-IgG rep1


title: 25-27N-H3K27ac-R2


title: Cas9 VEGFA2 48h HEK293T 500k PEI rep1


title: Cas9 VEGFA2 48h HEK293T 20k PEI rep1


title: 613DNA1


title: 609DNA1


title: Cas9 VEGFA2 48h HEK293T 1k PEI rep1


title: 608DNA1


title: 25-27N-H3K27ac-R1


title: Cas9 VEGFA2 48h HEK293T 100k PEI rep1


title: 607DNA1


title: CMM_13

description: 100 bp


title: 25-26N-H3K27ac-R1


title: Cas9 VEGFA2 48h HEK293T 100k-20pct-GFP PEI rep1


title: CMM_11

description: 100 bp


title: 606DNA1


title: Cas9 VEGFA2 48h HEK293T 100k-5pct-GFP PEI rep1


title: 25-26N-H3K27ac-R2


title: CMM_12

description: 100 bp


title: 25-32-H3K27ac-R2


title: CMM_10

description: 100 bp


title: 25-24N-H3K27ac-R1


title: CMM_08

description: 100 bp


title: Cas9 VEGFA1 96h HEK293T 500k PEI rep2


title: 604DNA1


title: 25-25N-H3K27ac-R1


title: 25-23N-H3K27ac-R2


title: CMM_09

description: 100 bp


title: CMM_14

description: 100 bp


title: 25-24N-H3K27ac-R2


title: Cas9 VEGFA2 24h HEK293T 500k PEI rep1


title: CMM_07

description: 100 bp


title: 602DNA1


title: Cas9 VEGFA2 48h HEK293T 100k-1pct-GFP PEI rep1


title: Cas9 VEGFA1 96h HEK293T 500k PEI rep1


title: 25-23N-H3K27ac-R1


title: CMM_06

description: 100 bp


title: 601DNA1


title: 600DNA1


title: Cas9 HEK4 96h HEK293T 500k PEI rep1


title: Cas9 HEK4 96h HEK293T 500k PEI batch2-2


title: CMM_05

description: 100 bp


title: 317DNA1


title: 25-25N-H3K27ac-R2


title: 605DNA1


title: Cas9 HEK4 96h HEK293T 500k PEI batch2-1


title: 25-22N-H3K27ac-R1


title: 603DNA1


title: Cas9 HEK4 96h HEK293T 500k PEI batch1


title: CMM_03

description: 100 bp


title: 25-21N-H3K27ac-R2


title: 315DNA1


title: 25-21N-H3K27ac-R1


title: 314DNA1


title: Cas9 HEK4 48h HEK293T 500k without-dsDNAase


title: CMM_02

description: 100 bp


title: 25-20T-H3K27ac-R2


title: CMM_01

description: 100 bp


title: 25-20T-H3K27ac-R1


title: Cas9 HEK4 72h HEK293T 500k PEI rep1


title: 313DNA1


title: 311DNA1


title: Cas9 HEK4 48h HEK293T 500k PEI rep1


title: CCN_10

description: 100 bp

source_name: cNormal

value: cNormal

value: Cutaneous


title: Cas9 HEK4 48h HEK293T 500k with-dsDNAase


title: 312DNA1


title: 25-22N-H3K27ac-R2

value: Non-neoplastic


title: CCN_09

description: 100 bp


title: 310DNA1

value: Female


title: CMM_04

description: 100 bp


title: CCN_08

description: 100 bp


title: Cas9 HEK4 48h HEK293T 500k ELEC rep1


title: CCN_07

description: 100 bp


title: 309DNA1


title: 25-20N-H3K27ac-R1


title: 25-19T-H3K27ac-R2


title: Cas9 HEK4 48h HEK293T 500k ELEC-noFACS-plasmid


title: 25-19T-H3K27ac-R1


title: 308DNA1


title: CCN_06

description: 100 bp


title: CCN_05

description: 100 bp


title: 25-20N-H3K27ac-R2


title: 25-19N-H3K27ac-R2


title: Cas9 HEK4 48h HEK293T 500k ELEC-noFACS-RNP


title: 25-19N-H3K27ac-R1


title: 306DNA1


title: Cas9 HEK4 12h HEK293T 500k PEI rep1


title: Cas9 HEK4 24h HEK293T 500k PEI rep1


title: 25-18T-H3K27ac-R1


title: 305DNA1


title: 25-18T-H3K27ac-R2


title: CCN_04

description: 100 bp


title: CCN_02

description: 100 bp


title: Cas9 HEK3 96h HEK293T 500k PEI rep2


title: Cas9 HEK3 96h HEK293T 500k PEI rep1


title: 304DNA1


title: CCN_01

description: 100 bp


title: 303DNA1


title: Cas9 HEK1 96h HEK293T 400k PEI rep1


title: CCM_14

description: 100 bp

source_name: cCAS

value: cCAS


title: Cas9 FANCF 96h HEK293T 500k PEI rep1


title: 302DNA1


title: 25-18N-H3K27ac-R2


title: 25-18N-H3K27ac-R1


title: 301DNA1


title: 307DNA1


title: 300DNA1


title: CCN_03

description: 100 bp


title: CCM_12

description: 100 bp


title: 25-17T-H3K27ac-R1


title: CBE VEGFA2 36h HEK293T 500k PEI rep1


title: CBE VEGFA2 24h HEK293T 500k PEI rep1


title: CCM_11

description: 100 bp


title: CBE VEGFA2 12h HEK293T 500k PEI rep1


title: 25-17N-H3K27ac-R2


title: CCM_08

description: 100 bp


title: CCM_10

description: 100 bp


title: 25-17N-H3K27ac-R1


title: 534DNA

value: birth


title: 529DNA


title: 531DNA


title: CBE HEK4 48h HEK293T 500k PEI rep1


title: 535DNA


title: CCM_09

description: 100 bp


title: CCM_07

description: 100 bp


title: 25-16T-H3K27ac-R1


title: 526DNA


title: CBE HEK4 36h HEK293T 500k PEI rep1


title: 523DNA


title: 25-16N-H3K27ac-R2


title: CCM_06

description: 100 bp


title: CCM_13

description: 100 bp


title: 25-17T-H3K27ac-R2


title: CBE VEGFA2 48h HEK293T 500k PEI rep1


title: CBE HEK4 24h HEK293T 500k PEI rep1-2


title: CBE HEK4 24h HEK293T 500k PEI rep1


title: CBE HEK4 12h HEK293T 500k PEI rep1


title: CCM_05

description: 100 bp


title: 25-16T-H3K27ac-R2


title: 522DNA


title: 25-15T-H3K27ac-R2


title: 521DNA


title: CCM_04

description: 100 bp


title: 25-15T-H3K27ac-R1


title: CBE-dCas9 HEK4 24h HEK293T 500k PEI rep2


title: 518DNA


title: CCM_03

description: 100 bp


title: 25-15N-H3K27ac-R2


title: CBE-dCas9 HEK4 24h HEK293T 500k PEI rep1


title: 513DNA


title: CCM_01

description: 100 bp


title: ABE VEGFA3 24h HEK293T 500k PEI rep2


title: 25-14T-H3K27ac-R2


title: CCM_02

description: 100 bp


title: 511DNA


title: ABE VEGFA3 24h HEK293T 500k PEI rep1


title: 510DNA


title: ABE HEK4 72h HEK293T 500k PEI rep1


title: cie_6

city: Fort Collins

first: Dylan

middle: T

last: Ammons

state: CO

address: 200 W Lake St

department: Clinical Sciences

institute: Colorado State University

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, and gene counting was completed using Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: CanFam3.1
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Duodenum

extract_protocol:
Biopsy samples were rinsed with ice cold phosphate buffered saline (PBS), then centrifuged at 400 rcf for 5 minutes. To dissociate epithelial cells, the samples were digested in Hanks’ balanced salt solution (HBSS) with 2 mM ethylenediaminetetraacetic acid (EDTA) and 10% fetal bovine for 30 minutes at 37C with intermittent vortexing. Following the EDTA digestion, the supernatant was removed, passed through a 70-uM cell strainer, and stored in HBSS with 5% FBS and 10 mM 4-(2-Hydroxyethyl)-1-piperazineëthanesulfonic acid (HEPES) on ice. The remaining tissue was resuspended in HBSS with collagenase type II at 250 U/mL and incubated for 30 minutes at 37C with intermittent vortexing. The two cell fractions were pooled together then passed through a 40-uM cell strainer. The pooled cells were resuspended in 4 mls HBSS and layered on top of 3 mls of Ficoll-Paque PLUS. Cells were isolated using density gradient centrifugation to enrich live cells for 30 minutes at 400 rcf with maximum acceleration and no brake. The cellular interface was aspirated then washed with PBS. If cell yield was low, all cells were pooled to obtain adequate cell numbers. To remove contaminating red blood cells, cells were incubated in ammonium-chloride-potassium lysis buffer at room temperature for 3 to 5 minutes. A final 15-minute centrifugation at 100 rcf at 8C was performed to remove small cellular debris and platelets. Lastly, cells were resuspended in 0.04% molecular grade bovine serum in PBS and transported to a Chromium iX instrument for cell capture. All samples were captured within 30 minutes of dissociation.
Library construction was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3ʹ Kit v3.1 protocol, 10x Genomics). Briefly, a Chromium iX instrument was used to pass cells and oligonucleotide coated gel beads at a limiting dilution to obtain a coupling of cells and beads in a 1:1 ratio. The cell-bead pair was then passed from an aqueous phase to an oil phase to form an emulsion. Within the emulsions, cells were lysed, and the oligonucleotide sequences on the gel beads pull down message RNA and other RNA molecules that have long adenosine stretches with an oligo-d(T) pull down. After hybridization, reverse transcription is completed to generate a cDNA library with each transcript now associated with a unique cell barcode and an Illumina R1 primer sequence.  Once cells were barcoded and unique molecular identifiers (UMIs) added, a standard Illumina library preparation kit was completed with SPRIselect used for fragment size selection. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: chronic inflammatory enteropathy (CIE)

value: Duodenum

value: Wt


title: cie_4

description: 10x Genomics


title: 25-16N-H3K27ac-R1

first: Chang

last: Lu

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

institute: Virginia Tech

source_name: Lung

value: Lung


title: 508DNA

value: Mouse midbrain


title: 25-14N-H3K27ac-R1


title: ABE HEK4 24h HEK293T 500k PEI rep1


title: 506DNA


title: cie_3

description: 10x Genomics


title: 505DNA

value: Control


title: 25-15N-H3K27ac-R1


title: ABE HEK4 24h HEK293T 500k PEI rep1-2


title: cie_2

description: 10x Genomics


title: 25-13T-H3K27ac-R2

value: Tumor


title: 503DNA

value: Male


title: 25-13T-H3K27ac-R1


title: h_3

description: 10x Genomics

value: healthy


title: ABE HEK4 12h HEK293T 500k PEI rep1


title: h_2

description: 10x Genomics


title: h_1

description: 10x Genomics


title: ABE HEK1 72h HEK293T 400k PEI rep1


title: 25-13N-H3K27ac-R1


title: 500DNA

value: Dieldrin


title: ABE HEK1 48h HEK293T 400k PEI rep1


title: 25-14N-H3K27ac-R2


title: ABE HEK4 48h HEK293T 500k PEI rep1


title: 329DNA


title: milk EVs, inulin 7

first: Wanjie

last: Yu

address: No. 2 Yuanmingyuan West Road

institute: Institute of Animal Science, Chinese Academy of Agricultural Sciences

data_processing:
In brief, raw data were converted from basic reads by base calling. Reads with 3’ adapters, without 5’ primer contaminants and poly (A), and ranging between 15 nt and 41 nt were kept to obtain clean reads. The Fastx_toolkit (version 0.0.13) was used to control the quality of the read. The NGSQC Toolkit (version 2.3.2) was used to filter reads containing N bases. Non-coding RNAs, including ribosomal RNAs, other small RNAs, and small nucleolar RNAs, were annotated by searching against the Rfam (v.10.1). The miRBase (v.21) database was used to identify miRNA and analyze their expression patterns.
Assembly: NCBI assembly Bos taurus (assembly ARS-UCD1.2), mirbase-22-release
Supplementary files format and content: miRNA.csv

organism: Bos taurus

source_name: milk

extract_protocol:
The RNA was isolated from the EV using the miRNeasy Mini Kit (cat. No. 217004, QIAGEN, Germany). The isolation process followed the manufacturer’s protocol. Briefly, EV samples were first lysed and homogenized in a highly denaturing guanidine-thiocyanate-containing buffer, which immediately inactivated RNases, ensuring the purification of intact RNA. By mixing with ethanol, the samples were loaded into an RNeasy Mini spin column. The total RNA bound to the membrane and contaminants were washed away. The eluted, high-quality RNA was collected and stored at -80 °C for further analysis.
Briefly, libraries were subjected to reverse transcription and amplification by connecting 3’ and 5’ adapters to the ends of RNA molecules using T4 RNA Ligase (catalog no. LR2D1132K, Epicentre, US). cDNA constructs were purified and recovered, and the libraries were subsequently checked and normalized.

value: milk

value: Inulin

tag: sample type

value: EV

tag: condition

value: subclinical mastitis


title: ABE HEK1 24h HEK293T 400k PEI rep1


title: 25-12-H3K27ac-R2

tag: tissue

tag: disease state

value: Non-neoplastic


title: 328DNA

first: Alison

last: Bernstein

address: 170 Freylinghuysen Rd

institute: Rutgers University

source_name: Mouse midbrain

value: Female


title: milk EVs, inulin 6


title: 25-12-H3K27ac-R1

tag: chip antibody


title: ABE HEK1 24h HEK293T 400k PEI rep1-2


title: milk EVs, inulin 5


title: 502DNA

value: birth


title: 326DNA


title: milk EVs, inulin 4


title: THLE2_shKDM1A_H3K4me1_CUTTAG

city: Shanghai

first: Boshi

last: Wang

address: No.800 Dongchuan Road

institute: Shanghai Cancer Institute

data_processing:
The sequencing reads obtained from the Illumina platform were subjected to quality control using FastQC (v0.11.9) to assess the quality of the reads.
Adapter trimming and read filtering were performed using Trim-galore (0.6.5-1).
The filtered reads were then aligned to the human genome (UCSC hg38) using Bowtie2 version 2.2.6.
The aligned reads were processed by MACS2 (v2.2.7.1) to call peaks and transformed to bigwig formatted files by bamCoverage function in Deeptools (v3.5.1) with default parameters.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: liver

extract_protocol:
The CUT&Tag experiments were performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech Co., Ltd., TD903) according to the manufacturer’s instructions.
The library was constructed by TruePrep® Index Kit V2 for Illumina kit and PCR amplification

value: liver

tag: cell type

value: liver cell line

value: H3K4me1 ab176877 Abcam


title: 325DNA


title: 25-10-H3K27ac-R2

city: Blacksburg

value: Lung


title: milk EVs, inulin 3


title: 25-13N-H3K27ac-R2


title: 321DNA

value: Mouse midbrain


title: milk EVs, inulin 2


title: cut187, mES cells

city: Xiamen

first: Xing

last: Xu

address: 422, Siming South Road

institute: Xiamen University

data_processing:
Trim_galore version 0.6.10 was utilized for initial sequence quality control and adapter sequence removal, applying parameters: -q 25 --phred33 --length 25 -e 0.1 --stringency 4.
Bowtie2 version 2.2.9 aligned the quality-trimmed paired-end sequencing data to reference genomes (GRCh38 for human and GRCm38 for mouse), using parameters: -p 10 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
Mitochondrial genes were excluded during alignment. Data were randomly downsampled to the desired depth for analysis. MACS2 version 2.2.6 executed peak calling with parameters: callpeak -g hs -p 1e-5 -f BEDPE --keep-dup all.
Peaks intersecting ENCODE blacklisted regions were excluded for both human and mouse analyses. For mES cells analysis, we capitalized on the low-input characteristic of DMF-ChIP-seq and proceeded with only 1M reads.
Assembly: hg38
Supplementary files format and content: Signal peak annotation bigwig file in bw file
Library strategy: CUT&Tag

source_name: embryo

growth_protocol: K562 cells were cultured in Dulbecco’s modified Eagle medium supplemented with 10% Fetal Bovine Serum and 1% penicillin-streptomycin. HeLa cells were cultured in Minimum Essential medium supplemented with 10% Fetal Bovine Serum and 1% penicillin-streptomycin. mES cells were cultured on 0.1% Gelatin pretreated culture flask and in Dulbecco’s modified Eagle medium supplemented with 15% Fetal Bovine Serum, 2 mM L-glutamine, 0.1mM Non-Essential Amino Acids, 0.1 mM 2-mercaptoethnol, and 1000U/mL recombinant leukemia inhibitory factor.

extract_protocol:
The DNAs of cells were released and enriched by using DNA extraction buffer (6 μL Buffer L/B, 0.3 μL Proteinase K, 1.2 μL DNA Extract Beads and 0.375 μL 1% F68)
DNA libraries were constructed according to CUT&Tag.

treatment_protocol: Recombinant leukemia inhibitory factor was withdrawn from medium for mES cells differentiation.

value: embryo

value: mES

value: embryonic stem cells

tag: genotype

value: WT


title: cut147, mES cells


title: milk EVs, inulin 1


title: HepG2_KDM1A_CUTTAG-2

value: HCC cells

tag: cut&tag antibody

value: KDM1A ab129195 Abcam


title: 320DNA

city: Piscataway

tag: strain

tag: Sex

value: Dieldrin


title: THLE2_shctr_H3K4me1_CUTTAG

tag: treatment

value: shctr


title: 319DNA

tag: age

value: Control


title: milk EVs, control 7

value: milk

value: EV

value: subclinical mastitis


title: 327DNA

value: Female

value: birth


title: THLE3_KDM1A_CUTTAG

value: liver

value: healthy liver cells


title: ABE HEK1 12h HEK293T 400k PEI rep1


title: cut189, mES cells


title: milk EVs, control 6


title: cut180, mES cells


title: 25-10-H3K27ac-R1

value: Lung

value: Non-neoplastic


title: THLE2_KDM1A_CUTTAG


title: 313DNA

value: Mouse midbrain


title: 314DNA


title: HepG2

data_processing:
Sequencing data obtained from the Illumina platform were subjected to quality control using FastQC (v0.11.9) to assess read quality.
Adapter trimming and read filtering were performed using Trim-galore (v0.6.5-1) with the following parameters: --phred33 --length 35 --stringency 3.
The resulting high-quality reads were aligned to the reference genome (hg38 for human) using Bowtie2 (v2.2.5) with the parameters: --very-sensitive -X 2000. The uniquely mapped reads were isolated by using samtools view function (samtools v1.6) under parameters:-f 2 -q 10 -b
The aligned reads were  transformed to bigwig formatted files by bamCoverage function in Deeptools (v3.5.1) with default parameters.
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
The ATAC experiments were performed using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme Biotech Co., Ltd., TD711) according to the manufacturer’s instructions.
The library was constructed by TruePrep® Index Kit V4 for Illumina kit and PCR amplification

value: HCC


title: 311DNA


title: milk EVs, control 5


title: Huh7


title: Whole blood, CPI0209 35mpk, 24hr, rep2 [4--2]

city: Boston

first: Jike

last: Cui

address: 470 Atlantic Ave

institute: MorphoSys AG

data_processing:
Sequencing reads were mapped to the genome using STAR2 and the transcript and gene read count quantification were performed using RSEM with default settings.
Assembly: hg38
Supplementary files format and content: read counts, csv file

source_name: whole blood

extract_protocol:
The RNA extractions were performed using PAXgene Blood RNA Kit following manufacturer’s instructions.
Library preparation with rRNA depletion and paired-end 150 base pair sequencing on an Illumina HiSeq was performed by GENEWIZ. Prior to sequencing, RNA integrity was assessed by 2100 Bioanalyser (Agilent) and concentration was assayed by Qubit.

value: whole blood

value: CB17-SCID with HT1376 cell line derived xenograft mice

value: CPI0209 35mpk 24hr


title: Whole blood, CPI0209 35mpk, 24hr, rep3 [4--3]


title: Whole blood, CPI0209 35mpk, 24hr, rep1 [4--1]


title: milk EVs, control 4


title: 310DNA

value: Dieldrin


title: milk EVs, control 3


title: THLE3

value: normal liver


title: Whole blood, CPI0209 35mpk, 6hr, rep3 [3--3]

value: CPI0209 35mpk 6hr


title: milk EVs, control 2

value: milk

value: Control


title: 306DNA


title: Huh7_KDM1A_CUTTAG

value: HCC cells

value: KDM1A ab129195 Abcam


title: THLE2


title: Whole blood, CPI0209 35mpk, 6hr, rep2 [3--2]


title: 304DNA

value: Female

value: birth


title: milk EVs, control 1

value: EV

value: subclinical mastitis


title: HepG2_shKDM1A_ATACseq

data_processing:
Sequencing data obtained from the Illumina platform were subjected to quality control using FastQC (v0.11.9) to assess read quality.
Adapter trimming and read filtering were performed using Trim-galore (v0.6.5-1) with the following parameters: --phred33 --length 35 --stringency 3.
The resulting high-quality reads were aligned to the reference genome (hg38 for human) using Bowtie2 (v2.2.5) with the parameters: --very-sensitive -X 2000.
The aligned reads were  transformed to bigwig formatted files by bamCoverage function in Deeptools (v3.5.1) with default parameters.
Assembly: hg38
Supplementary files format and content: bigwig

value: liver


title: 303DNA

value: Mouse midbrain


title: Whole blood, CPI0209 35mpk, 6hr, rep1 [3--1]


title: HepG2_shctr_ATACseq

value: HCC


title: SRPK RNAi , biological replicate 3 (S16)

city: Cambridge

first: Yukiko

last: Yamashita

state: MA

address: 455 main ST

institute: Whitehead Institute for Biomedical Research

data_processing:
Paired-end reads (250 x 250 bp) were align using STAR aligner (v. 2.7.1a)
gene count was generate using featureCounts
Assembly: Dmel Release 6.37
Supplementary files format and content: FeatureCount output

organism: Drosophila melanogaster

source_name: testis

growth_protocol: All fly stocks were raised on standard Bloomington medium at 25°C, and young flies (1- to 3-day-old adults) were used for all experiments

extract_protocol:
Total RNA was extracted from dissected testes by Trizol extraction.
Libraries were prepared using the KAPA Biosystems RNA HyperPrep Kit with RiboErase. 500 ng of total RNA was used for library construction.

value: testis

value: SRPK RNAi


title: Whole blood, CPI0209 35mpk, 1hr, rep3 [2--3]

value: whole blood

value: CB17-SCID with HT1376 cell line derived xenograft mice

value: CPI0209 35mpk 1hr


title: 302DNA

value: Dieldrin


title: U2af38 RNAi, biological replicate 3 (S14)

value: U2af38 RNAi


title: HepG2_GSK_LSD1_H3K4me1_CUTTAG

value: H3K4me1 ab176877 Abcam


title: Control, biological replicate 3 (S13)

value: Control


title: Whole blood, CPI0209 35mpk, 1hr, rep2 [2--2]


title: Whole blood, CPI0209 35mpk, 1hr, rep1 [2--1]


title: SRPK RNAi , biological replicate 2 (S10)


title: HepG2_SP2509_H3K4me1_CUTTAG


title: Whole blood, veh, rep3 [1--3]

value: Vehicle


title: U2af38 RNAi , biological replicate 2 (S8)


title: Whole blood, veh, rep2 [1--2]


title: HepG2_ctr_H3K4me1_CUTTAG


title: Control, biological replicate 2 (S7)


title: Day5_f3

city: Palo Alto

first: Avnesh

last: Thakor

state: California

address: 3155 Porter Dr

department: Radiology

institute: Stanford Medicine

description:
f05_3
female at day 5

data_processing:
Sequenced reads were trimmed for adaptor sequence,
Then mapped to mouse genome Mus Musculus using HISTAT
HTSeq was used to generate the raw read counts
DESeq2 was used for differential gene expression analysis
Assembly: (GRCm39/mm39)
Supplementary files format and content: tab-delimited text file include FPKM values for all samples
Supplementary files format and content: tab-delimited text file include raw counts for all samples

source_name: kidney

extract_protocol:
total RNA was extracted from each replicate using the RNAeasy minikit (qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

value: wt

value: female

value: cisplatin

tag: time


title: HCC_PDX_SP2509_H3K4me1_CUTTAG

source_name: HCC-PDX

value: HCC-PDX

tag: cell line


title: Day5_f2

description:
f05_2
female at day 5


title: SRPK RNAi, biological replicate 1 (S4)


title: U2af38 RNAi, biological replicate 1 (S2)


title: HCC_PDX_Ctr_H3K4me1_CUTTAG


title: Day5_f4

description:
f05_4
female at day 5


title: In_vivo_scRNA_seq_PBS

city: New Haven

first: Rong

last: Fan

state: Connecticut

address: 55 Prospect St.

institute: Yale University

data_processing:
For scRNA-seq, the raw fastq files were generated and demultiplexed by CeleScope rna from Singleron (version 3.0.1) and primary data analysis was performed with CeleScope (version 1.10.0) using a custom reference package based on reference genome (Mus_musculus_ensembl_92)
For ATAC+Gene multiomics, the Cell Ranger ARC v2.0.2 (10x Genomics) was utilized to perform sample demultiplexing, barcode processing, identification of open chromatin regions, and simultaneous counting of transcripts and peak accessibility in single cells from the sequenced data.
Assembly: Mus_musculus_ensembl_92
Supplementary files format and content: Gene expression matrix
Supplementary files format and content: Combined Gene+ATAC expression matrix and ATAC fragments and annotation files

source_name: Tumor

growth_protocol: Tumors were collected and digested, and tumor-infiltrating PMEL T cells were enriched and sorted out for scRNA-seq

extract_protocol:
In vivo scRNA-seq was performed using the GEXSCOPE Single Cell RNA Library Kit Cell V2 reagents (Singleron Biotechnologies GmbH). In vitro single-cell ATAC+gene multiome was performed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics, Cat# PN-1000283)
Libraries were constructed according to the protocols provided by the aforementioned kits.
scRNA-seq and single cell ATAC+Gene multiomics

value: Tumor

value: T cells

value: PBS


title: 301DNA

value: Mouse midbrain

value: Female

value: birth


title: mut-FTO-3

first: Zhang

last: Min

address: Jiangwangmiao Street, Xuanwu District

institute: Hospital for Skin Diseases

data_processing:
Sequence alignment of Clean Reads to a reference genome using Hisat2 to obtain information on the position on the reference genome or gene, as well as information on sequence features specific to the sequenced sample. Gene transcription generates precursor mRNAs (pre-mRNAs) that are spliced in a variety of ways, selecting different exons to produce different mature mRNAs, which are translated into different proteins, constituting a diversity of biological traits. This post-transcriptional mRNA processing is called variable splicing or selective splicing. StringTie was used to splice the Hisat2 comparison results, and the type of variable splicing present in each sample and the corresponding expression was obtained by ASprofile software.
Assembly: mm10
Supplementary files format and content: All_gene_counts.list

source_name: Cell

extract_protocol:
Nucleic acid extraction was accomplished using the (Tengen DP411, CLB + Adderall RN40 CTAB + Adderall RN40, Tengen DP762-T1C) kit/TRIzol reagent.
The first step is to purify and break the mRNA, the second step is to synthesize the first strand of cDNA, the third step is to synthesize the second strand of cDNA and purify the second strand product, the fourth step is to repair the ends and add A to the 3'-ends, the fifth step is to ligate the junctions, the sixth step is to purify the ligated product and select the fragment, the seventh step is to amplify the ligated product, the eighth step is to purify the PCR product, and the final step is to perform a quality check on the library by using the Qsep-400 method.

value: Cell

value: HaCat cells

value: keratinocytes


title: In_vivo_scRNA_seq_Fc_IL4


title: Day5_f1

description:
f05_1
female at day 5


title: Day5_m3

description:
m05_3
male at day 5

value: male


title: mut-FTO-2


title: Day5_m4

description:
m05_4
male at day 5


title: HepG2_GSK2879552_H3K4me1_CUTTAG

value: liver

value: HCC

value: H3K4me1 ab176877 Abcam


title: Control, biological replicate 1 (S1)

value: testis

value: Control


title: 25-14T-H3K27ac-R1

value: Lung


title: 300DNA

value: Dieldrin


title: Day5_m2

description:
m05_2
male at day 5

value: kidney

value: wt

value: cisplatin


title: E11_5_CVG_H3K27ac_Rep3

city: Augusta

first: Lin

last: Gan

state: Geogia

address: 1120 15th Street

department: Department of Neuroscience & Regenerative Medicine

institute: Augusta University

data_processing:
Data was preprocessed with quality controls using FastQC, and then Bowtie2 aligned peaks.
After that, peaks were called with SEACR with the significance cut-off q-value <=0.01.
Peak annotation and mapping in relation to the proximal genes were performed using ChIP seeker. Finally, peaks were visualized by IGV.
Assembly: mm10
Supplementary files format and content: narrowPeak (except for IgG sample)
Library strategy: CUT&Tag

source_name: Mouse CVGs

extract_protocol:
E11.5 CVGs were dissected and extracted nuclei immediately by incubating in the NE Buffer for 10 min on ice.
To prepare the library, 21ul DNA fragments was removed to PCR tube, to which 2 ul of barcoded i5 and i7 primers and 25 ul CUTANA High Fidelity 2x PCR Master Mix (EpiCypher, #15-1018) were added. PCR was performed using the following conditions: 72 °C for 5 min, 98 °C for 30 sec, and 20 (can be changed depending on experience with the sample) cycles of 98 °C for 10 sec, 63 °C for 10 sec, followed by an extra 1 min extension at 72 °C. The PCR product was analyzed on an Agilent Fragment Analyzer. Combined DNA libraries were cleaned up using AMPure XP beads (Beckman Coulter, #A63880) following the manufacturer’s instructions.

value: Mouse CVGs


title: E11_5_CVG_H3K27ac_Rep2


title: FTO-3


title: FTO-2


title: PFF_AZD_HTO

city: Birmingham

first: Yong

state: AL

address: 1918 University Blvd

department: Cell, Developmental and Integrative Biology

institute: University of Alabama at Birmingham

description:
10x Genomics
Hashtag-derived oligonucleotide (HTO)
HTO library: read 1 file contains cell barcode and UMI, read2 file contains Hashtag Antibody Derived Tag reads
PFFAZD_barcodes.tsv
PFFAZD_features.tsv
PFFAZD_matrix.mtx

library_source: other

data_processing:
Raw base call files were demultiplexed into FASTQ files. Sequencing files were processed and mapped to mm10, and count matrices were extracted using the Cell Ranger Single Cell Software (v 7.1.0) .
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: protein

source_name: midbrain

extract_protocol:
Mononuclear cells were isolated for sequencing as described above with 3-5 ventral midbrains pooled per sample and sorted for CD45+ live cells on a BD FACsAria. Sorted CD45+ cells were resuspended in DPBS supplemented with 0.04% w/v BSA.
Single Cell 3′ Reagent Kit V3.1 was used in conjunction with TotalSeqB antibodies to generate 3' gene expression library and HTO library. Single cells and beads containing barcoded DNA oligos were captured into oil droplets to generate the gel bead-in-emulsion (GEM) by 10x Chromium controller. The poly-A RNA from the cell lysate in GEM was reverse-transcripted to cDNA. Libraries were constructed according to the manufacturer’s instructions

value: midbrain

value: CD45+ cells

value: Line 61 mice

value: PFF + AZD1480

tag: library type

value: HTO

tag: hto

value: TotalSeq-B0301 anti mouse Hashtag, TotalSeq-B0302 anti mouse Hashtag2, TotalSeq-B0303 anti mouse Hashtag3, TotalSeq-B0304  anti mouse Hashtag4, TotalSeq-B0305  anti mouse Hashtag5


title: E11_5_CVG_H3K27ac_Rep1


title: PFF-VH_HTO

description:
10x Genomics
Hashtag-derived oligonucleotide (HTO)
HTO library: read 1 file contains cell barcode and UMI, read2 file contains Hashtag Antibody Derived Tag reads
PFFVH_barcodes.tsv
PFFVH_features.tsv
PFFVH_matrix.mtx

value: PFF + VH

value: TotalSeq-B0301 anti mouse Hashtag, TotalSeq-B0302 anti mouse Hashtag2, TotalSeq-B0303 anti mouse Hashtag3, TotalSeq-B0304  anti mouse Hashtag4


title: PFF-AZD_GEX

description:
10x Genomics
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI, read2 file contains transcript
PFFAZD_barcodes.tsv
PFFAZD_features.tsv
PFFAZD_matrix.mtx

value: mRNA


title: mut-FTO-1

city: Nanjing

value: Cell

value: HaCat cells

value: keratinocytes


title: Whole blood, veh, rep1 [1--1]

value: whole blood

value: CB17-SCID with HT1376 cell line derived xenograft mice

value: Vehicle


title: PFF-VH_GEX

description:
10x Genomics
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI, read2 file contains transcript
PFFVH_barcodes.tsv
PFFVH_features.tsv
PFFVH_matrix.mtx


title: Vector-3


title: E11_5_CVG_H3K27me3_Rep1


title: E11_5_CVG_H3K27me3_Rep3


title: Day3_f2

description:
f03_2
female at day 3

value: kidney

value: wt

value: female

value: cisplatin


title: E11_5_CVG_H3K27me3_Rep2

value: Mouse CVGs